Merge pull request #70 from adrientaudiere/dev

fix : fix a bug in multitax_bar_pq
adrientaudiere · Jan 22, 2024 · a0e6aa2 · a0e6aa2
2 parents bc9458a + 4e76442
commit a0e6aa2
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diff --git a/R/plot_functions.R b/R/plot_functions.R
@@ -2443,7 +2443,7 @@ multitax_bar_pq <- function(
       summarise(Abundance = sum(Abundance)) %>% 
       filter(Abundance > 0)
 
-    psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3, fact)], 
+    psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3)], 
                       by = join_by("OTU" == "OTU"), multiple = 
                         "first")
 

diff --git a/vignettes/tengeler.Rmd b/vignettes/tengeler.Rmd
@@ -6,6 +6,7 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
+
 This tutorial explore a phyloseq version of the dataset from Tengeler et al. (2020) available in the `mia` package.
 
 ```{r, include = FALSE}
@@ -158,6 +159,12 @@ biplot_pq(subset_taxa_pq(ten, taxa_sums(ten) > 3000),
 multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status")
 ```
 
+
+```{r}
+multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status",
+                nb_seq = FALSE, log10trans = FALSE)
+```
+
 # Differential abundance analysis
 
 ```{r}